Structure and conformation of the sodium chloride salt of N-t-Boc-Phenylalanyl-Proline (Boc-Phe-Pro·NaCl) and the dihydrate of N-t-Boc-Tyrosyl-Proline (Boc-Tyr-Pro·2H2O)

The structure and conformation of the salt of N-t-Boc-Phenylalanyl-Proline (Boc-Phe-Pro·NaCl) (C₁₉H₂₆N₂O₅NaCl) (compound 2) and the dihydrate of N-t-Boc-Tyrosyl-Proline (Boc-Tyr-Pro·2H₂O) (C₁₉H₃₀O₈N₂) (compound 1) have been investigated with X-ray crystallographic and spectroscopic methods. Boc-Phe-Pro·NaCl crystallizeds in an extended trans conformation in the space groupP2₁ with cell dimensionsa=7.961 (3),b=10.045(2), andc=13.495(4). One intermolecular hydrogen bond and one intramolecular hydrogen bond was observed for the dipeptide salt. Boc-Tyr-Pro·2H₂O crystallized in an extended trans conformation in the space group P2₁ with cell dimensionsa=7.964(1),b=10.011(1), andc=13.853(2). Six intermolecular hydrogen bonds were observed for Boc-Tyr-Pro·2H₂O. The conformation of both dipeptides reflect collagen-type of proline-compounds. The puckering mode of the pyrrolidine ring of the proline residues can be described as an approximate C₂ half-chair symmetry having an A conformation with the Cγ atom located exo and Cβ atom located endo relative to the carboxamide group, i.e., γ/β T.Cis-trans isomerism was observed in the NMR spectra of both dipeptides with a predominance for the extended side chain for the phenylalanyl and tyrosyl residues, respectively.     

Crystal structure and spectroscopic studies of a new organic monohydrogenmonophosphate dihydrate

The crystal synthesis and structure of a new organic monohydrogenmophosphate (3,4‐Cl₂‐CH₂C₆H₃NH₃)₂HPO₄·2H₂O are reported. This compound crystallizes in the monoclinic P2₁/n with a = 9.081(7) Å, b = 6.501(5) Å, c = 35.423(12) Å, β = 91.09(5)°, V = 2090.9(2) ų, and Z = 4. Crystal structure was solved and refined to R = 0.042, using 2543 independent reflections. It can be described by inorganic layers, including the HPO₄^‐ anions and the H₂O molecules, parallel to (a, b) planes and situated at z = 0 and z = 1/2. The interlayer spacing is occupied by the organic molecules which perform different interactions around the 3D network cohesion. A characterization of this compound by solid‐state (¹³C, ³¹P) MAS NMR and IR spectroscopies is also reported. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

A comparative study on structure and conformation of three hydroxybenzylamine ligands

Structure and conformation of three tridentate ligands are determined. All these three compounds crystallize in different space groups, the details are as follows: Bis[(3,5-dimethyl,2-hydroxy)-2-hydroxy-5-methoxy]benzylcyclohexylamine (DHBC): monoclinic I2/a (a = 17.691(1) Å, b = 9.707(1) Å, c = 24.235(2) Å, = 91.028(1)°); bis[(3,5-dimethyl,2-hydroxy)-2-hydroxy-5-bromo]benzylcyclohexylamine (DHBrBC): tetragonal P4₁2₁2 (a = b = 12.1138(1) Å, c = 28.485(1) Å) and bis[(3,5-dimethyl,2-hydroxy)-2-hydroxy-5-bromo]benzylmethylamine (DHBrBM): triclinic (a = 5.228(1), b = 12.364(1) Å, c = 13.234(1) Å, = 94.04(1)°, = 95.72(1),° = 95.90(1)°). The cyclohexane rings in DHBC and DHBrBC assume chair conformation. Both the phenyl rings are planar in all the molecules and orient at angles of 75.5(1)°, 62.2(1)°, and 53.9(2)°, respectively with each other. The bond angles around N atom show the sp³ character. Inter- and intramolecular O–HN and O–HO types of hydrogen bondings stabilize the molecules in the unit cell in addition to van der Waals forces.     

Dynamical and structural properties of titanium-decorated fullerene: A computer simulation study

We have investigated a material made of C₆₀Ti₆H₁₂ molecules using the classical molecular dynamic simulation. The system was studied in a wide range of temperatures, from solid to fluid. Several physical characteristics of endohedral fullerene were calculated for various temperatures: the mean square displacement, the translational and angular velocity autocorrelation function, the translational diffusion coefficient and the Lindemann index. We have observed a reduction in the rotational freedom of fullerene decorated with TiH₂ functionality groups in comparison with the pure fullerene sample.     

Terahertz time-domain spectroscopy: A new tool for the study of glasses in the far infrared

Terahertz time-domain transmission spectroscopy was used to obtain the absorption coefficients and refractive indices of polycrystalline quartz, amorphous silica, Pyrex and BK7 glasses. The results were analyzed in terms of the power-law model of far-infrared absorption. Evidence of the Boson peak was seen in the absorption spectra. Relationships were observed between THz absorption and refractive indices on the one hand, and glass structure and properties on the other. THz TDS is demonstrated to be a useful tool in the study of far-infrared transmission properties of glasses, producing low-noise, high resolution measurements of absorption coefficients and refractive indices.     

Synthesis,growth and characterization of a new nonlinear optical crystal: l‐arginine maleate dihydrate

A new nonlinear optical material L‐arginine maleate dihydrate, C₆H₁₄N₄O₂,C₄H₄O₄,2H₂O (LAMD) was synthesized and single crystals were grown by slow cooling and also by slow evaporation method at constant temperature from its aqueous solution. Quality and size of the crystals are found to be dependent on pH of the solution and best crystals were obtained at pH = 4. Single crystal X‐ray diffraction analysis reveal that the crystal lattice of LAMD is triclinic with unit cell parameters a = 5.264(3)Å, b = 8.039(3)Å, c = 9.784(3)Å, α = 106.19(3)°, β = 97.24(3)°, γ = 101.66(2)°. Second harmonic generation efficiency is found to be about 6.8 times that of quartz. It is optically transparent down to 300 nm and possesses a large optical window between 300–2000 nm. The compound is thermally stable up to 93.4 °C. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Synthesis and structural conformation of N‐substituted 1,4‐dihyropyridine derivatives

N‐(Phenyl)‐3,5‐dicarbethoxy‐2,6‐dimethyl‐4‐(phenyl)‐1,4‐dihydropyridine (A) and N‐(4‐methoxy phenyl)‐‐3,5 dicarbethoxy‐2,6 dimethyl‐4‐(3‐nitro phenyl)‐1,4‐dihydropyridine (B) has been synthesized as per scheme and characterized by the X‐ray diffraction method. The compound A crystallizes in monoclinic space group P21/c with cell parameters a = 9.2770(11)Å, b = 8.6410(5)Å, c = 27.601(3)Å, β = 97.724(3)°, Z = 4. The compound B crystallizes in monoclinic space group P21/c with cell parameters a = 11.229(6), b = 12.746(7)Å, c =17.606(6)Å, β = 104.531(3)°, Z = 4. The structures exhibit both intra and intermolecular hydrogen bonds. Dihydropyridine ring of both the compounds adopt a flat boat conformation. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Synthesis of a new dibenzo-14-crown-4 lariat ether and structure of its sodium perrhenate complex

A dibenzo-14-crown-4 ether with a novel monooxyacetone sidearm is prepared and its structure with sodium perrhenate is determined. The structure crystallizes in P2₁/c with cell dimensions: a = 8.107(2) Å, b = 28.138(3) Å, c = 10.293(2) Å, and = 104.173(9)°; giving a volume of 2276.6(7) ų. This structure is compared to other sodium complexes of dibenzo-14-crown-4 lariat ethers and is found to be the only one with intramolecular bonding between the sidearm and the cation. Possible reasons for this observation are discussed.     

A structural study of sol–gel and melt-quenched phosphate-based glasses

Phosphate-based glasses have recently attracted much interest as a new generation of biomaterials because of their ability to react and dissolve in the physiological environment and eventually to be replaced by regenerated hard or soft tissue. A series of phosphate-based glasses containing 45 mol% P₂O₅ and various amounts of CaO and Na₂O were synthesized by sol–gel and melt-quenching techniques. A comparison between the structure of the sol–gel glass and the structure of the analogous melt-quenched glasses has been undertaken. A broad-based characterization approach combining different techniques has been used to investigate the short-range structure of the glasses and the effect of adding modifier oxides to the network structure (conventional and high energy X-ray diffraction, infra-red spectroscopy, ³¹P solid state magic angle spinning NMR spectroscopy). Sol–gel and melt-quenched glasses appear to have a similar structure, showing similar Qⁿ distributions and atomic correlations.     

A MAS NMR structural study of cadmium phosphate glasses

Cadmium phosphate glasses, of general formula xCdO(1−x)P₂O₅ (0.25?x?0.6), have been prepared by melting in alumina crucibles, with resulting dissolution of up to 6.4 mol% Al₂O₃. The local structure in these glasses has been studied using ³¹P, ²⁷Al and ¹¹³Cd nuclear magnetic resonance. The distribution of [PO₄]Qⁿ species as a function of composition has been shown to follow the simple binary model. The rate of change of the chemical shift of the ³¹P species in the Q² environment depends on the bond order, which in turn reflects the extent of double bonding between phosphorus and oxygen.     

Synthesis and structural characterization of the dinuclear bis(glutarato)bis(urea)copper(II)complex, dihydrate

The complex [Cu(OOC-(CH₂)₃-COO)(O=C(NH₂)₂]₂·2H₂O has been synthesized and characterized by X-ray crystallography. It crystallizes in the triclinic system P-1 with a = 8.003(2) ?, b = 8.611(2) ?, c = 8.620(2) ?, α = 96.14(3)°, β = 116.66(2)°, γ = 105.66(4)° and V = 492.9(3) ?³. The structure consists of discrete centrosymmetric binuclear units and water molecules. The Cu(II) ions adopt a square-pyramidal coordination with four oxygen atoms of four bridging carboxylate and one carbonyl oxygen of the monodentate urea ligand. There is a very strong interaction between the two copper centers in binuclear entities (CuCu: 2.6266(15) ?).     

Effect of fluoride ion incorporation on the structural aspects of barium-sodium borosilicate glasses

Barium-sodium borosilicate glasses containing upto 6 wt% fluoride ions were prepared by conventional melt quench method and characterized by ¹⁹F, ²⁹Si and ¹¹B nuclear magnetic resonance (NMR) techniques.¹⁹F NMR studies have confirmed the presence of mainly linkages like F-Si(n) or F-B(n) along with F-Ba(n). Their relative concentrations are unaffected by F⁻ content in the glass. Incorporation of fluoride ions in the glass is associated with significant reduction in the nonbridging oxygen concentration attached to silicon, as revealed by the increase in the concentration of Q³ structural units of silicon at the expense of Q² structural units. ¹¹B NMR studies have established that the relative concentrations of BO₃ structural units are higher for F⁻ ion containing glasses compared to the one without F⁻ ion incorporation. The observed increase in the relative concentrations of Q³ structural units of silicon and BO₃ structural units with fluoride ion incorporation in the glass has been attributed to the formation of F-Ba(n) type of linkages, thereby reducing the concentration of network modifying cations for breaking the Si-O-Si/B-O-B linkages. Formation of such structural units weakens the glass network thereby decreasing the glass transition temperatures.     

Optical and structural properties of new chalcohalide glasses

New class of chalcohalide glasses has been prepared in the GeS₂–In₂S₃–CsI system with regard to their potential non-linear properties. The study of glass-forming region was undertaken to select glassy compositions, which present high non-linear (NL) optical properties with a low two-photon absorption. Thermal analyses, structural examination by Raman spectroscopy, non-linear optical measurements were investigated as a function of CsI contents. Introduction of CsI has shifted the band-gap edge towards the blue region of the absorption optical spectrum and therefore has limited the two-photon absorption. Their NL refractive index n₂ are 60 times higher than silica glasses without any NL absorption. Moreover, second harmonic signal was observed in thermally poled samples similar to silica glass. However, this second order non-linearity is not temporally stable.     

Effect of BaO addition on the structural aspects and thermophysical properties of sodium borosilicate glasses

Sodium borosilicate glasses containing different amounts of BaO were prepared by a conventional melt quench method and characterized for their structural aspects by ²⁹Si, ¹¹B NMR and IR spectroscopy. From ²⁹Si MAS NMR studies, it has been inferred that these glasses consist of Q² and Q³ structural units of silicon and that the addition of BaO results in the marginal conversion of Q³ to Q² structural units. There is no direct interaction between Ba²⁺ ions and boron structural units, as revealed by the identical values of the relative concentration of BO₃ and BO₄ structural units and quadrupolar coupling constant values for the BO₃ structural units. The identical values of glass transition temperature and vibrational frequencies corresponding to Si–O–Si/Si–O–B and B–O linkages of all the samples further support this. As the borosilicate network is unaffected, the systematic increase in the values of thermal expansion coefficient with increase in BaO content has been attributed to the increase in the relative concentration of less rigid Ba–O linkages compared to the more rigid Si–O and B–O linkages in the glass. Such studies will be useful for the development of matrices for the management of nuclear waste generated during the reprocessing of the spent fuel from thoria based reactors.     

FIBSIMS: A review of secondary ion mass spectrometry for analytical dual beam focussed ion beam instruments

Secondary ion mass spectrometry (SIMS) is a well-known technique for 3D chemical mapping at the nanoscale, with detection sensitivity in the range of ppm or even ppb. Energy dispersive X-ray spectroscopy (EDS) is the standard chemical analysis and imaging technique in modern scanning electron microscopes (SEM), and related dual-beam focussed ion beam (FIBSEM) instruments. Contrary to the use of an electron beam, in the past the ion beam in FIBSEMs has predominantly been used for local milling or deposition of material. Here, we review the emerging FIBSIMS technique which exploits the focused ion beam as an analytical probe, providing the capability to perform secondary ion mass spectrometry measurements on FIBSEM instruments: secondary ions, sputtered by the FIB, are collected and selected according to their mass by a mass spectrometer. In this way a complete 3D chemical analysis with high lateral resolution <?50 nm and a depth resolution <?10 nm is attainable.We first report on the historical developments of both SIMS and FIB techniques and review recent developments in both instruments. We then review the physics of interaction for incident particles using Monte Carlo simulations. Next, the components of modern FIBSIMS instruments, from the primary ion generation in the liquid metal source in the FIB column, the focussing optics, the sputtered ion extraction optics, to the different mass spectrometer types are all detailed. The advantages and disadvantages of parallel and serial mass selection in terms of data acquisition and interpretation are highlighted, while the effects of pressure in the FIBSEM, acceleration voltage, ion take-off angles and charge compensation techniques on the analysis results are then discussed. The capabilities of FIBSIMS in terms of sensitivity, lateral and depth resolution and mass resolution are reviewed. Different data acquisition strategies related to dwell time, binning and beam control strategies as well as roughness and edge effects are discussed. Data analysis routines for mass identification based on isotope ratios and molecular fragments are outlined. Application examples are then presented for the fields of thin films, polycrystalline metals, batteries, cultural heritage materials, isotope labelling, and geological materials. Finally, FIBSIMS is compared to EDS, and the potential of the technique for correlative microscopy with other FIBSEM based imaging techniques is discussed.     

A computer simulation study of the structural similarities between fluoroberyllate and alkaline earth silicate melts

The three-dimensional structures of molten alkali fluoroberyllates and alkaline earth silicates at the meta-composition have been analyzed by molecular dynamics simulation. A quantitative similarity was obtained between these two systems in respect of their partial distribution functions and the coordination numbers of their constituent ion pairs.     

Surface morphology,structural and optical properties of polar and non-polar ZnO thin films: A comparative study

The polar and non-polar ZnO thin films were fabricated on cubic MgO (1 1 1) and (0 0 1) substrates by plasma-assisted molecular beam epitaxy. Based on X-ray diffraction analysis, the ZnO thin films grown on MgO (1 1 1) and (1 0 0) substrates exhibit the polar c-plane and non-polar m-plane orientation, respectively. Comparing with the c-plane ZnO film, the non-polar m-plane ZnO film shows cross-hatched stripes-like morphology, lower surface roughness and slower growth rate. However, low-temperature photoluminescence measurement indicates the m-plane ZnO film has a stronger 3.31 eV emission, which is considered to be related to stacking faults. Meanwhile, stronger band tails absorbance of the m-plane ZnO film is observed in optical absorption spectrum.     

Crystallization field study for the formation of single phase sodium clinoptilolite: Batch composition,seed and temperature effects

Although clinoptilolite is the most abundant zeolite mineral in nature, its synthesis under laboratory conditions has been difficult. A partial crystallization field study was done for the synthesis of clinoptilolite based on a nominal batch composition of 2.1Na₂O:Al₂O₃:10Si₂O:110H₂O to delineate the limits of composition and temperature within which sodium clinoptilolite can be produced as a single phase in high yields. Effects of temperature, SiO₂/Al₂O₃ molar ratio in the batch composition, and the use of different raw materials in batch preparation were studied. The need for the use of seed crystals for reproducible synthesis of clinoptilolite was established. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Network hydrogen bonding: the crystal and molecular structure of cubane-1,3,5,7-tetracarboxylic acid dihydrate

The structure of cubane-1,3,5,7-tetracarboxylic acid dihydrate (1) has been determined. It crystallizes in the space groupP2₁/c with cell dimensionsa=6.503(1),b=19.173(1),c=10.527(1) Å, β=101.60(1). The details of this structure have reaffirmed the fact that the cubane skeleton is a flexible entity which reflects its steric and electronic environment. Of the four carboxylic acid groups three adopt asyn conformation while the fourth adopts ananti conformation. The orientation of these groups with respect to the cubane skeleton is reflected in the C?C bond lengths. Those C?C bonds which are perpendicular to the carboxylic acid groups are the longest and those which are most nearly eclipsed are the shortest in the cubane skeleton. In all cases it is the C=O rather than the C?O bond which is most nearly eclipsed with a C?C bond. The tetrahedral orientation of the substitutents does not express itself in a three dimensional supramolecular assembly; however, all four carboxylic acid groups are involved in very strong donor hydrogen bonds which result in a two dimensional array parallel to (100). An additional surprising results is the fact that none of the four substituents participate in traditional hydrogen bonded carboxylic acid dimeric moieties.